Skip to content

Instantly share code, notes, and snippets.

View johnsolk's full-sized avatar

Lisa K. Johnson johnsolk

85 followers · 70 following
View GitHub Profile
@johnsolk
johnsolk / MMETSP_diginorm_streaming_v_not.csv
Created July 12, 2016 19:44
Comparison with transrate of Trinity trascriptome assemblies from 3 MMETSP samples, diginorm streaming vs. not
assembly n_seqs smallest largest n_bases p_contigs_with_CRBB p_refs_with_CRBB reference_coverage
SRR1300409.Trinity.streaming.fixed.fasta_no_orphans 30605 224 4134 19238075 0.97543 0.92568 0.85853
SRR1300409.streaming.fixed.fasta 30457 224 4134 19243907 0.98276 0.93851 0.89009
SRR1300409.Trinity.fixed.fasta 30771 224 4210 19279950 0.98096 0.94858 0.89449
SRR1300402.streaming.fixed.fasta 35128 224 13921 22716553 0.9928 0.98108 0.94234
SRR1300402.not.fixed.fasta 35101 224 13528 22584802 0.99282 0.98024 0.93656
SRR1300410.Trinity.streaming.fixed.fasta 9316 224 4094 5055897 0.99141 0.96962 0.93397
SRR1300410.Trinity.fixed.fasta 9414 224 4096 5077982 0.98959 0.97993 0.94012
@johnsolk
johnsolk / formatting_annotations.sh
Created August 29, 2016 01:53
formatting transcriptome annotations for merging with lists of differentially expressed lists contig ID
sed 's_|_-_g' uniprot_sprot.blastx.outfmt6.sig > uniprot_sprot.blastx.outfmt6.fixed.sig
cut -f 1,2,17 uniprot_sprot.blastx.outfmt6.fixed.sig > uniprot_sprot.blastx.outfmt6.fixed.genes.sig
touch uniprot_P_ast_annotations_mansour_hits100DE.tab
for i in $(cut -f 2 P_ast_RNAseq_25pptv35ppt_top100DE.tab); do grep ${i/_/-} uniprot_sprot.blastx.outfmt6.fixed.genes.sig >> uniprot_P_ast_annotations_mansour_hits100DE.tab; done
sed 's/\-/\_/1' uniprot_P_ast_annotations_mansour_hits100DE.tab > uniprot_P_ast_annotations_mansour_hits100DE.fixed.tab
@johnsolk
johnsolk / example_gff3_dammit_output
Last active March 13, 2017 22:39
dammit_annotations_parsing
##gff-version 3.2.1
Transcript_0 transdecoder CDS 1664 2062 . + . ID=cds.Transcript_0|m.1;Parent=Transcript_0|m.1
Transcript_0 transdecoder exon 1 2064 . + . ID=Transcript_0|m.1.exon1;Parent=Transcript_0|m.1
Transcript_0 transdecoder five_prime_UTR 1 1663 . + . ID=Transcript_0|m.1.utr5p1;Parent=Transcript_0|m.1
Transcript_0 transdecoder gene 1 2064 . + . ID=Transcript_0|g.1;Name=ORF%20Transcript_0%7Cg.1%20Transcript_0%7Cm.1%20type%3A3prime_partial%20len%3A134%20%28%2B%29
Transcript_0 transdecoder mRNA 1 2064 . + . ID=Transcript_0|m.1;Parent=Transcript_0|g.1;Name=ORF%20Transcript_0%7Cg.1%20Transcript_0%7Cm.1%20type%3A3prime_partial%20len%3A134%20%28%2B%29
Transcript_0 transdecoder three_prime_UTR 2063 2064 . + . ID=Transcript_0|m.1.utr3p1;Parent=Transcript_0|m.1
Transcript_100002 transdecoder CDS 1 1047 . + . ID=cds.Transcript_100002|m.114344;Parent=Transcript_100002|m.114344
Transcript_100002 transdecoder CDS 1411 1722 . + . ID=cds.Transcript_100002|m.114346;Parent=Transcript_100002|m.114346
Transcript_100002
@johnsolk
johnsolk / fastq_to_fasta.py
Created June 14, 2017 23:07
# checks for redundancies in record headers
# converts fastq to fasta format
import screed
f = open('porecamp_killifish.fasta','wb')
for n,r in enumerate(screed.open('porecamp_killifish.fastq')):
if r.name in s:
continue
else:
@johnsolk
johnsolk / ncbi_urlprediction.py
Last active September 5, 2017 21:32
"""
From Luiz Irber.
Takes an SRA accession and determines the location of the .sra data file for automated or downloading.
Follows this format: ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/{SRR|ERR|DRR}/<first 6 characters of accession>/<accession>/<accession>.sra
Format according to NCBI utility handbook: https://www.ncbi.nlm.nih.gov/books/NBK158899/
"""
def sra_url(accession):
"""Returns predicted URL given SRA accession as input."""
accession = accession.upper()
@johnsolk
johnsolk / oysterriver_readnums
Last active September 12, 2017 20:10
[ljcohen@dev-intel14 trim]$ for i in $(find /mnt/scratch/ljcohen/oysterriver/ -name "*left.fq"); do echo $i; done
/mnt/scratch/ljcohen/oysterriver/ERR1674585/trinity/ERR1674585.left.fq
/mnt/scratch/ljcohen/oysterriver/ERR489297/trinity/ERR489297.left.fq
/mnt/scratch/ljcohen/oysterriver/DRR036858/trinity/DRR036858.left.fq
/mnt/scratch/ljcohen/oysterriver/DRR069093/trinity/DRR069093.left.fq
/mnt/scratch/ljcohen/oysterriver/DRR053698/trinity/DRR053698.left.fq
/mnt/scratch/ljcohen/oysterriver/DRR031870/trinity/DRR031870.left.fq
/mnt/scratch/ljcohen/oysterriver/SRR2016923/trinity/SRR2016923.left.fq
/mnt/scratch/ljcohen/oysterriver/ERR058009/trinity/ERR058009.left.fq
/mnt/scratch/ljcohen/oysterriver/SRR2086412/trinity/SRR2086412.left.fq
@johnsolk
johnsolk / replace.sh
Created September 26, 2017 07:16
#replace IUPAC ambiguous characters in all fasta files in a directory
for i in $(ls *.fa); do sed -i -e 's/[YRWSKMDVHBX]/N/g' $i; done
@johnsolk
johnsolk / msu_hpcc_commands.sh
Last active September 26, 2017 21:38
# delete block of jobs in queue all starting with specific digits in Job ID
qstat -u ljcohen | grep "472526" | cut -d "." -f1 | xargs qdel
@johnsolk
johnsolk / fasta_to_table.py
Last active October 12, 2017 17:27
# From within a py3 virtualenv
# or
# sudo pip install screed
# source ~/bin/py3/bin/activate
import screed
with open("table.txt",'w') as fq:
for r in screed.open('trinity.nema.full.fasta'):
fq.write(r.name+"\n")
@johnsolk
johnsolk / mmetsp_loops.sh
Created October 26, 2017 00:12
for file in $(find . -name "*.fasta.dammit.gff3"); do echo $file; cut -f1 $file | uniq | wc -l; done > ~/MMETSP/assembly_evaluation_data/total_contigs
for file in $(find `pwd` -name "*.fasta.renamed.fasta.dammit.gff3");
do
base=$(basename $file .renamed.fasta.dammit.gff3)
new=$base.dammit.gff3
echo cp $file /mnt/scratch/ljcohen/mmetsp_dammit/cp/gff3/$new
done