Installing HTSeq on python (mac)

[qoiopipq]

I am trying to install HTSeq-0.6.1 on mac. I downloaded and setup python2.7 from Anaconda2, which include key packages: Numpy, Scipy, etc

When I tried to install HTSeq on this python, it couldn't complete the installation (it stop at the step "changing mode of build/..."):

svi-3216:HTSeq-0.6.1 aliu$ /Users/aliu/anaconda2/bin/python setup.py build
running build
running build_py
creating build
creating build/lib.macosx-10.5-x86_64-2.7
creating build/lib.macosx-10.5-x86_64-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq
creating build/lib.macosx-10.5-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.macosx-10.5-x86_64-2.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.macosx-10.5-x86_64-2.7
creating build/temp.macosx-10.5-x86_64-2.7/src
gcc -fno-strict-aliasing -I/Users/aliu/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/aliu/anaconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/aliu/anaconda2/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.5-x86_64-2.7/src/_HTSeq.o -w
gcc -bundle -undefined dynamic_lookup -L/Users/aliu/anaconda2/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/src/_HTSeq.o -L/Users/aliu/anaconda2/lib -o build/lib.macosx-10.5-x86_64-2.7/HTSeq/_HTSeq.so
building 'HTSeq._StepVector' extension
gcc -fno-strict-aliasing -I/Users/aliu/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/aliu/anaconda2/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.5-x86_64-2.7/src/StepVector_wrap.o -w
g++ -bundle -undefined dynamic_lookup -L/Users/aliu/anaconda2/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/src/StepVector_wrap.o -L/Users/aliu/anaconda2/lib -o build/lib.macosx-10.5-x86_64-2.7/HTSeq/_StepVector.so
running build_scripts
creating build/scripts-2.7
copying and adjusting scripts/htseq-qa -> build/scripts-2.7
copying and adjusting scripts/htseq-count -> build/scripts-2.7
changing mode of build/scripts-2.7/htseq-qa from 644 to 755
changing mode of build/scripts-2.7/htseq-count from 644 to 755
svi-3216:HTSeq-0.6.1 aliu$

svi-3216:~ aliu$ ./anaconda2/bin/python
Python 2.7.11 |Anaconda 4.0.0 (x86_64)| (default, Dec 6 2015, 18:57:58)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import HTSeq
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named HTSeq
>>>

Any suggestions would be great! Thanks!

[wdecoster]

According to the website (http://www-huber.embl.de/HTSeq/doc/install.html) you have to execute the following

python setup.py build
sudo python setup.py install

or to just install for you as user and not as root for all users:
python setup.py install --user

[dpryan]

You can skip "python setup.py build" and just directly "python setup.py --user install" (or "pip install --user ."). The latter calls the former internally.

[qoiopipq]

Thanks! Solved this by just typing "python setup.py install --user".

[dpryan]

BTW, since you're already using anaconda, you could also "conda install -c bioconda htseq". That'd be faster and pretty much guaranteed to work.

[qoiopipq]

I tried to run htseq count (using anaconda) on one of my sorted bam files, which is around 2.2 GB, but it is very slow.... It's already been 1 day and it's still running. Can I do anything to speed up the process? Will sorting the bam file in names rather than coordinates help?

this is the command I used:
python /Users/aliu/anaconda2/bin/htseq-count -f bam -r pos Liver_accepted_hits_sorted.bam /Users/aliu/Mus_musculus.DEXSeq.chr.gff > liver2.txt

and also I got this warning:
Warning: No features of type 'exon' found.

Thanks!

[dpryan]

HTSeq-count probably isn't running at all. Have a look at the GFF file, it's likely the case that the "exon" entries have been renamed "exonic_bin" or something like that, so you'll need to specify that when running htseq-count. Presuming you want these counts as input with DEXSeq, you should use the wrapper around htseq-count that comes with DEXSeq (there's a bit in the vignette about this).

[qoiopipq]

I had a quick look at my GFF file, it has a column contains either "aggregate_gene" or "exonic_part", I guess "exonic_part" is the "exonic_bin" you mentioned. So I will specify it and give it a go.

$ less genes_dexseq.gff | head
chr1 dexseq_prepare_annotation.py aggregate_gene 3214482 3671498 . gene_id "Xkr4"
chr1 dexseq_prepare_annotation.py exonic_part 3214482 3216968 . transcripts "NM_001011874"; exonic_part_number "001"; gene_id "Xkr4"
chr1 dexseq_prepare_annotation.py exonic_part 3421702 3421901 . transcripts "NM_001011874"; exonic_part_number "002"; gene_id "Xkr4"
chr1 dexseq_prepare_annotation.py exonic_part 3670552 3671498 . transcripts "NM_001011874"; exonic_part_number "003"; gene_id "Xkr4"
chr1 dexseq_prepare_annotation.py aggregate_gene 4290846 4409241 . gene_id "Rp1"
chr1 dexseq_prepare_annotation.py exonic_part 4290846 4293012 . transcripts "NM_001195662"; exonic_part_number "001"; gene_id "Rp1"
chr1 dexseq_prepare_annotation.py exonic_part 4343507 4350091 . transcripts "NM_011283"; exonic_part_number "002"; gene_id "Rp1"

[wdecoster]

Good morning. Indeed, the warning is likely your problem and you need -t exonic_part in your command. -t exon is the default, that's why htseq-count couldn't find a single feature of type 'exon'.

[qoiopipq]

Finally, it worked!! I used the htseq-count that comes with DEXSeq without specifying 'exonic_part'. Actually, the 3rd column in Dmel.BDGP5.25.62.DEXSeq.chr.gff (sample dataset in the vignette) contains 'exonic_part' for exons and 'aggregate_gene' for genes:

chr2L Drosophila_melanogaster.BDGP5.25.62.gtf.gz aggregate_gene 7529 9484 . + . gene_id "FBgn0031208"
chr2L Drosophila_melanogaster.BDGP5.25.62.gtf.gz exonic_part 7529 8116 . + . transcripts "FBtr0300689+FBtr0300690"; exonic_part_number "001"; gene_id "FBgn0031208"
chr2L Drosophila_melanogaster.BDGP5.25.62.gtf.gz exonic_part 8193 8589 . + . transcripts "FBtr0300689+FBtr0300690"; exonic_part_number "002"; gene_id "FBgn0031208"

So, just put in this: python ...path to dexseq/dexseq_count.py [options] annotation.gff sorted.bam output.txt

Cheers!