small fixes

Author: gitliver

.gitignore

@@ -12,3 +12,4 @@ doc/*.pdf
 *.DS_Store
 notes
 tmp*
+old

README.md

@@ -24,7 +24,7 @@ The following programs must be in your `PATH`:
 Pandora depends on the following Python modules:
 
 - [Biopython](http://biopython.org/wiki/Main_Page)
-- [Pandas](http://pandas.pydata.org/)
+- [Pandas >= 0.20.1](http://pandas.pydata.org/) (note: older versions of Pandas, such as 0.18.1, will throw an error)
 - scipy
 
 The exact list, with versions, is provided in the `requirements.txt` file.

pandora.py

@@ -155,7 +155,7 @@ def get_arg():
         args.steps += '6'
 
     # cast as various bools as ints
-    for name in 'gzip verbose noclean noSGE orfblast'.split():
+    for name in 'gzip verbose noclean noSGE orfblast hpc'.split():
         setattr(args, name, int(getattr(args, name, 0)))
 
     # set bam file to abs path
@@ -245,8 +245,8 @@ def scan_main(args):
     d = {
              '1': '{args.scripts}/scripts/host_separation.py --scripts {args.scripts} -1 {args.mate1} -2 {args.mate2} --bam {args.bam} --threads {args.map_threads} --single {args.single} --refstar {args.refstar} --refbowtie {args.refbowtie} --gzip {args.gzip} --verbose {args.verbose} --noclean {args.noclean} --gtf {args.gtf}'.format(args=args),
              '2': '{args.scripts}/scripts/assembly.py --scripts {args.scripts} --single {args.single} --trinitymem {args.trinitymem} --trinitycores {args.trinitycores} --trinitythreshold {args.trinitycontigthreshold} --verbose {args.verbose} --noclean {args.noclean}'.format(args=args),
-             '3': '{args.scripts}/scripts/blast_wrapper.py --scripts {args.scripts} --threshold {args.contigthreshold} --db {args.blastdb} --threads {args.blast_threads} --id {args.identifier} --filelength {args.blastchunk} --verbose {args.verbose} --noclean {args.noclean} --nosge {args.noSGE}'.format(args=args),
-             '4': '{args.scripts}/scripts/orf_discovery.py --scripts {args.scripts} --id {args.identifier} --threshold {args.orfthreshold} --db {args.pblastdb} --blast {args.orfblast} --verbose {args.verbose} --noclean {args.noclean} --hpc {args.hpc}'.format(args=args),
+             '3': '{args.scripts}/scripts/blast_wrapper.py --scripts {args.scripts} --threshold {args.contigthreshold} --db {args.blastdb} --threads {args.blast_threads} --id {args.identifier} --filelength {args.blastchunk} --verbose {args.verbose} --noclean {args.noclean} --nosge {args.noSGE} --hpc {args.hpc}'.format(args=args),
+             '4': '{args.scripts}/scripts/orf_discovery.py --scripts {args.scripts} --id {args.identifier} --threshold {args.orfthreshold} --db {args.pblastdb} --blast {args.orfblast} --verbose {args.verbose} --noclean {args.noclean}'.format(args=args),
              '5': '{args.scripts}/scripts/makereport.py --scripts {args.scripts} --id {args.identifier} --verbose {args.verbose} --blacklist {args.blacklist} --taxid2names {args.taxid2names}'.format(args=args),
              '6': '{args.scripts}/scripts/makereport.py --outputdir report_ifilter --input blast/ifilter.concat.txt --scripts {args.scripts} --id {args.identifier} --verbose {args.verbose} --blacklist {args.blacklist} --taxid2names {args.taxid2names}'.format(args=args)
     }