Python lab

an_exon.fa

>where_is_the_exon
ATCAATTCGATTCCAAAACTGTTTTTAACTGTATTGCTAAGCTGCCTTCCACTAGGTTGG
TCAGGAAGGATAGTAGAGACAGAGGAAATGGCAGAAGGGACTGGGGGGGTGGGGACAAGA
TGCTGGCTCTGTTGCATTTTGAAGGCCACATCTGCCAGCCTGGGAGTGGCCTGTGGTGGC
CAGGCAACCCAGCTTGATGTTGCCTCTTCTGTCCTGAGGATGGAACAGAGGCAGGTGAGA
AGCTTTCTGTGGCTGCTGCAGCAAAACCAACCTATGACCAGGGGCTTTGGCTGCCATTGC
CCTCCCTCCAGCCAGAAGTAAGGAGAAGGGAGCCATGCTTTTGGTGGGTAAGCTCCGCGA
ACAAGAACTGTGGCCCTGGGAGCTTTACTCTCAGTCCTAGCTTCTCCAGGAGAGGGTCAG
CCACTGGATGCTTGGAGTCCACACTAACAGCACAACTGATTCTCGGCAGCTGACGACGGG
AGTGGAGTATATAGTCACTGTGAAGATTGGCTGGACCAAATGCAAGAGGAATGACACGAG
CAATTCTTCCTGCCCCCTGCAAAGCAAGAAGCTGAGAAAGGTGTGTAGTGGAAGTCATCC
CAAAGGGACTTGTGAAGTGAATATTTTAAAAAGCAACAGCTAGAAGTTGGCAGTTTTGCC
ACTTGTGTGGATTGGGGCCAGCTGGGGCCCAGCCCTGGGGCTGTCTGGCACCTCCTGAGG
CACCTGGGTGAAGGAGGGAGGCTTTATATTTGGGCTGGTACAGCCCTGCACCCAGGCCTC
TGGTTGCCTGGACCCTTCTCCAACCTGGCCTGCTCCCCAGACCCTCTGCGTGAAAGCAGT
GGTTCCCTTTCCTTGGGGTCCTTCTTCTGTCTTCTTTCTCCCTCTCCAGGTCTCTAAGGT
TGTCCAATTTCCTCCTTGTTCCCTTCTATTTTTCCTGGTCCATGAGTGGCACCCCTTGAA
AGCTGGCAGATACAAGGGGCTCCCCCATGCCTGGGGAGGTGCAGGAGGAGGTAACGATGC
TATTGCTCCTTGCTGGCCTGCCTGGCCCACATGACAGGGTCCGGCCAGGCCATAGACTCC
AGGTTCACCTGCTGTGGGTCCCAAGTGGCTGGGTAGGGGGAAGACAGGGTGACATTCCTG
TTCCAGACTGGCACTCCTTTCTGTTTCTACCCTTGACTGTGGGCAGCTCCCCTCTCTGCC
CATGGGGTTCATGAGCAGCCACAGGGAGAGACCTGGGGAACAGGTGCCTGTTGCTTGCCT
TTGAAAAATACTTCCCCCAAAGTCTGTTTTCTTTCTTCTTCTACAGAGTTTAATTTGCGA
GTCTTTGATATACACCATGCCCTGGATAAACTATTTCCAGCTCTGGAACAATTCCTGTCT
GGAGGCCGAGCATGTGGGCAGAAACCTCAGATGAGGGCTCATATGATTGAGTTGTGCACT
GGCTGTTATTAAACTGTAAAGGATCA

lab1.py

import random
length = int(input("Length of sequence: "))
sequence = ""
for i in range(0, length):
  sequence += random.choice(['A', 'G', 'C', 'T'])
print sequence

lab1_3.py

# How to run:
# cat Stockholm-Test.txt | python lab1_3.py

import fileinput
import re
sequence_names = []

for line in fileinput.input():
  # if re.search(r'^([A-Z]|[0-9])+\.[0-9]\/[0-9]+-[0-9]+\s+(G|A|C|U|-)+\s?$', line):
  #   sequence_names.append(line.split()[0])

  # if not re.search(r'^[A-Z].*', line):
  #   sequence_names.append(line.split()[0])

  # if not re.search(r'^(#|\s|\/).*', line):
  #   sequence_names.append(line.split()[0])

  # if line.strip() and not (line.startswith('#') or line.startswith('/')):
  #   sequence_names.append(line.split()[0])

  if line.strip() and not line.startswith('#') and not line.startswith('/'):
    sequence_name, sequence = line.split()
    sequence_names.append(sequence_name)

print str(len(sequence_names)) + '\n'
print '\n'.join(sequence_names)

lab1_4.py

# How to run:
# python lab1_4.py < Stockholm-Test.txt

import sys
import re

def is_valid_sequence_line(line):
  return re.search(r'^(\w|-|\/)+\s+(\w|-|\.)+', line)

def print_line_in_fasta_format(line):
  sequence_name, sequence = line.split()
  print '>' + sequence_name

  sequence_chunks = re.findall('.{1,60}', sequence)
  print '\n'.join(sequence_chunks)

def main():
  for line in sys.stdin.readlines():
    if is_valid_sequence_line(line):
      print_line_in_fasta_format(line)

if __name__ == "__main__":
  main()

lab1_5.py

# How to run:
# python translate.py < translate.fa

import sys
import re

codontable = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W',
}

def prepareForNewSequence():
  global ongoing_sequence, longest_orf, sequence, stops

  ongoing_sequence = False
  longest_orf = ""
  sequence = ""
  stops = []

def calculateLongestOrf():
  global longest_orf, stops

  stops += [m.start() for m in re.finditer('(TAA|TAG|TGA)', sequence.upper())]
  # This is the _final_ stops, when no codon's found.
  # Example with sequence of length 10:
  # 10 - 4 => 6,7,8. Two nucleotides left: 9,10, in which, cannot be translated.
  stops += [len(sequence)-4, len(sequence)-3, len(sequence)-2]

  for start in range(0,len(sequence)):
    if start in stops:
      # We cannot start with a stop, shift
      continue

    for stop in stops:
      if stop > start and (stop - start) % 3 == 0:
        test_orf = sequence[start:stop]

        if len(test_orf) > len(longest_orf):
          longest_orf = test_orf

        break # when first relevant stop is found, shift

def translateLongestOrf():
  translated = ""
  for i in range(0,len(longest_orf),3):
    translated += codontable.get(longest_orf[i:i+3].upper(), 'X')

  translated_chunks = re.findall('.{1,60}', translated)
  print '>' + sequence_name
  print '\n'.join(translated_chunks)

def main():
  global sequence, sequence_name, ongoing_sequence

  prepareForNewSequence()
  for line in sys.stdin.readlines():
    newSequenceMatch = re.search(r'^>(\w+).*', line) # returns match object if match else nothing

    # newSequenceMatch will be casted to a boolean implicitly
    if newSequenceMatch:
      # Finish current sequence before parsing a new
      if ongoing_sequence:
        calculateLongestOrf()
        translateLongestOrf()
        prepareForNewSequence()

      # group(1) will take what's inside the parenthesis in the regex above, i.e. (.+), in this case the name of the sequence
      # group(0) will take the whole line
      sequence_name = newSequenceMatch.group(1)
      ongoing_sequence = True
    elif ongoing_sequence:
      sequence += line.strip()
  # for end

  if ongoing_sequence:
    # Always calculate and translate at end of file when sequence is found
    calculateLongestOrf()
    translateLongestOrf()

if __name__ == "__main__":
  main()

longseqs.sthlm

# STOCKHOLM 1.0
gene4711	ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
hubba		ACGTACGTACGTACGTACGTACGTANNNNNNNNNNTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTT
gene4712	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
//

shortseqs.sthlm

# STOCKHOLM 1.0
only10chars	ACGTACGTAC
emptysequence
onenucleotide	----------
//

Stockholm-Test.txt

# STOCKHOLM 1.0

#=GF AC   RF00107
#=GF ID   FinP
#=GF DE   FinP
#=GF AU   Griffiths-Jones SR
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:9917389
#=GF GA   45.00
#=GF TC   50.80
#=GF NC   43.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   9917389
#=GF RT   Degradation of FinP antisense RNA from F-like plasmids: the RNA-binding
#=GF RT   protein, FinO, protects FinP from ribonuclease E.
#=GF RA   Jerome LJ, van Biesen T, Frost LS
#=GF RL   J Mol Biol 1999;285:1457-1473.
#=GF RN   [2]
#=GF RM   14633993
#=GF RT   FinO is an RNA chaperone that facilitates sense-antisense RNA
#=GF RT   interactions.
#=GF RA   Arthur DC, Ghetu AF, Gubbins MJ, Edwards RA, Frost LS, Glover JN
#=GF RL   EMBO J 2003;22:6346-6355.
#=GF CC   The FinOP system regulates the transfer of F-like plasmids. FinP encodes
#=GF CC   an antisense RNA product that is complementary to part of the 5' UTR of
#=GF CC   the traJ mRNA. The traJ gene encodes a protein required for transcription
#=GF CC   from the major transfer promoter, pY. The FinO protein is essential for
#=GF CC   effective repression, acting by binding to FinP and protecting it from
#=GF CC   RNase E degradation.
#=GF WK   FinP
#=GF SQ   6


AE006471.1/61593-61518 GACACAUAGGAACCUCCUCA--AAGGAUUCUAUGGACAGUCGAUGCAGGGAGU-GACAG-CUCCCUGUAUCGGCGAUUUA
X55896.1/1041-966      CACACAUAGGAACCUCCUCA--AAGGAUUCUAUG-ACAGUCGAUGCAGGGAGG-GACAAGCUCCCUGCAUCGGCGAUUUU
U01159.2/1039-961      GAUACAUAGGAACCUCCUCACAAAGGAUUCUAUGGACAGUCGAUGCAGGGAGUUCACGU-CUCCCUGCAUCGGCGAUUUU
X55894.1/1036-958      GAUACAUAGGAACCUCCUCACAAAGGAUUCUAUGGACAGUCGAUGCAGGGAGGAGAGAA-CUCCCUGCAUCGGCGAUUUU
AF389529.1/1113-1037   GAUACACAGGAGCCUCCUCA--AAGGAUUCUAUGGGUAGUCGAUGCAGGGAGG-GACCAACUCCCUGCAUCGGCGAUUUA
M20941.1/217-140       GAUACAUAGGAACCUCCUCUCAAAGGAUUCUAUGGACAGUCGAUGCGGGGAGGUCGCU--CUCCCUGCAUCGGCGAUUUU
#=GC SS_cons           ::::<<<<<<<-<<<________>>>->>>>>>>----<<<<<<<<<<<<<<_______.>>>>>>>>>>>>>>::::::
#=GC RF                gAuACauaGgaACCuCCUCAcAAaGGAuuCuauGGAcAGuCGauGCaGGGaGgugAcaa.CuCCCuGCauCGgCGAUUUu
//