Mercurial > repos > jay > pdaug_tsvtofasta
changeset 4:87b77f2ddb0c draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 8b18552f6d2b2261efebe1075ff4c18a295b94dd"
| author | jay |
|---|---|
| date | Tue, 29 Dec 2020 18:13:00 +0000 |
| parents | e873a5224d1e |
| children | f93187136dfb |
| files | PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml PDAUG_TSVtoFASTA/test-data/test1/Negative.fasta PDAUG_TSVtoFASTA/test-data/test1/Positive.fasta |
| diffstat | 4 files changed, 6 insertions(+), 50 deletions(-) [+] |
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--- a/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Tue Dec 29 03:57:13 2020 +0000 +++ b/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Tue Dec 29 18:13:00 2020 +0000 @@ -21,14 +21,16 @@ l.append(line.split('\t')[1].strip('\n').strip('\r')) l = list(set(l)) + print(l) + for line in lines: - if l[0] in line.split('\t')[1].strip('\n').strip('\r'): + if l[1] in line.split('\t')[1].strip('\n').strip('\r'): n= n+1 of1.write('>peptide_'+str(n)+'_'+str(l[0])+'\n') of1.write(line.split('\t')[0]+'\n') - if l[1] in line.split('\t')[1].strip('\n').strip('\r'): + if l[0] in line.split('\t')[1].strip('\n').strip('\r'): m= m+1 of2.write('>peptide_'+str(m)+'_'+str(l[1])+'\n') of2.write(line.split('\t')[0]+'\n')
--- a/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml Tue Dec 29 03:57:13 2020 +0000 +++ b/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml Tue Dec 29 18:13:00 2020 +0000 @@ -49,8 +49,8 @@ <test> <param name="InFile" value="test1.tsv"/> <param name="Method" value="WithClassLabel"/> - <output name="OutFile1" file="test1/Positive.fasta"/> - <output name="OutFile2" file="test1/Negative.fasta"/> + <output name="OutFile1" file="test1/FirstDataFile.fasta"/> + <output name="OutFile2" file="test1/SecondDataFile.fasta"/> </test> <test> <param name="InFile" value="test2.tsv"/>
--- a/PDAUG_TSVtoFASTA/test-data/test1/Negative.fasta Tue Dec 29 03:57:13 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->peptide_1 -GLFDIVKKVVGALG ->peptide_2 -KLLKLLKKKLLK ->peptide_3 -KLLLLKLLK ->peptide_4 -GLFDIVKKVVGALG ->peptide_5 -GLFDIVKKVVGALG ->peptide_6 -KLLKLLKKKLLK ->peptide_7 -KLLLLKLLK ->peptide_8 -GLFDIVKKVVGALG ->peptide_9 -GLFDIVKKVVGALG ->peptide_10 -KLLKLLKKKLLK ->peptide_11 -KLLLLKLLK ->peptide_12 -GLFDIVKKVVGALG
--- a/PDAUG_TSVtoFASTA/test-data/test1/Positive.fasta Tue Dec 29 03:57:13 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ ->peptide_1 -GLFDIVKKVVGALG ->peptide_2 -KLLKLLKKKLLK ->peptide_3 -KLLLLKLLK ->peptide_4 -GLFDIVKKVVGALG ->peptide_5 -GLFDIVKKVVGALG ->peptide_6 -KLLKLLKKKLLK ->peptide_7 -KLLLLKLLK ->peptide_8 -GLFDIVKKVVGALG ->peptide_9 -KLLKLLKKKLLK ->peptide_10 -KLLLLKLLK ->peptide_11 -GLFDIVKKVVGALG