Tabea Kischka Tabea-K

## sort_blastn_by_bitscore.sh
sort -k1,1 -k12,12gr -k11,11g -k3,3gr blastout.txt | sort -u -k1,1 --merge > bestHits

## add_numbers_to_fastq_headers.sh
awk 'BEGIN{s=0}{if(NR % 4==1){print $0"_"s; s=s+1}else{print $0}}'

## get_fastq_seq_lengths.sh
awk '{if(NR % 4==1){printf $0"\t"}else if(NR % 4==2){print length($0)}}'

## pdf2png.sh
#!/usr/bin/env bash
convert -density 300  -resize 25% $1 $2

## fastq_check_lengths.py
#!/usr/bin/env python

import sys
import os
import argparse

q_ascii = "!#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~"
q_ascii += '"'

def id_error(line_no, name, line):

## fastqgrep.py
#!/usr/bin/env python
'''
This script extracts specific fastq sequences
from a multi-fastq sequence file, with the ID's
of the sequences to be extracted in a txt file.
'''
import sys
import argparse
import os

## draw_aln.py
#!/usr/bin/env python
"""
Creates a pdf alignment
"""

import sys
import os
import tempfile

input_filename = sys.argv[1]

## maf2fasta.py
#!/usr/bin/env python
"""
Created by Tabea Kischka at 2015-01-27 10:34:05

converts a last maf alignment into a fasta alignment
"""
import sys

path_to_alignio = '/home/tabeah/Scripts/alignio-maf'

## nr_of_common_lines_per_column.sh
#!/usr/bin/env bash
# Prints the number of identical rows between different columns for two
# csv files. The first argument is the column number which should be used.
# For example, you can compare the IDs given in a csv file.

cut -f $1 $2 | sort > .file1
cut -f $1 $3 | sort > .file2


# With no options, comm produces three-column output.

## fasta2fastq.sh
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' | awk 'BEGIN {RS = ">" ; FS = "\n"} NR > 1 {print "@"$1"\n"$2"\n+"$1"\n"gensub(/./, "I", "g", $2)}'
	#!/usr/bin/env python

	import sys
	import os
	import argparse

	q_ascii = "!#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{\|}~"
	q_ascii += '"'

	def id_error(line_no, name, line):
	#!/usr/bin/env python
	'''
	This script extracts specific fastq sequences
	from a multi-fastq sequence file, with the ID's
	of the sequences to be extracted in a txt file.
	'''
	import sys
	import argparse
	import os
	#!/usr/bin/env python
	"""
	Creates a pdf alignment
	"""

	import sys
	import os
	import tempfile

	input_filename = sys.argv[1]
	#!/usr/bin/env python
	"""
	Created by Tabea Kischka at 2015-01-27 10:34:05

	converts a last maf alignment into a fasta alignment
	"""
	import sys

	path_to_alignio = '/home/tabeah/Scripts/alignio-maf'
	#!/usr/bin/env bash
	# Prints the number of identical rows between different columns for two
	# csv files. The first argument is the column number which should be used.
	# For example, you can compare the IDs given in a csv file.

	cut -f $1 $2 \| sort > .file1
	cut -f $1 $3 \| sort > .file2


	# With no options, comm produces three-column output.